I've done pretty much what you suggest - using a waterproof connector to install the Kev Mod.
Extend both ends of the cut blue/black wire (solder ad heat-shrink) so they reach the under seat area and connect to a female 2-way Superseal connector. Fit the male end of the Superseal connector to the Kev Mod.
As you suggest prepare a second male Superseal connector with a bridging wire joining its two terminals, so if you need to remove the Kev Mod you can just plug this in to return everything to normal.
I use a Velcro sticky pad to stick the Kev Mod to the bike under the seat, so it can be easily pulled out and hung out the side of the seat so it can be tuned whilst on the move.
Weatherproof Superseal connectors can be bought cheaply
here (don’t, whatever you do, be tempted to pay Touratech prices for them!)